Plant rna transport and rna-directed rna polymerase proteins

ABSTRACT

This invention relates to an isolated nucleic acid fragment encoding a RNA-directed RNA polymerase. The invention also relates to the construction of a chimeric gene encoding all or a substantial portion of the RNA-directed RNA polymerase, in sense or antisense orientation, wherein expression of the chimeric gene results in production of altered levels of the RNA-directed RNA polymerase in a transformed host cell.

This application is a continuation-in-part of U.S. application Ser. No.09/958,109, filed Oct. 2, 2001, now allowed and herein incorporated byreference, which is a 35 U.S.C. 371 national filing of InternationalApplication No. PCT/US00/09105, filed Apr. 6, 2000, which claims thebenefit of U.S. Provisional Application No. 60/128,094, filed Apr. 7,1999.

FIELD OF THE INVENTION

This invention is in the field of plant molecular biology. Morespecifically, this invention pertains to nucleic acid fragments encodingRNA-directed RNA polymerase proteins in plants and seeds.

BACKGROUND OF THE INVENTION

The phloem of a plant is a vascular tissue that is responsible fordistributing the products of photosynthesis, nutrients and hormones toplant tissues and organs. Associated with the phloem are sieve elementsand companion cells. Mature sieve cells are enucleate and must rely onphysically connected companion cells (via a branched plasmodesmata) toprovide many physiological functions. Sieve cells and companion cellstogether serve to deliver proteins into the phloem. Research has shownthat specific mRNA molecules can be found in the plasmodesmatasuggesting that there are mechanisms that participate in mRNA transportthrough the sieve cell-companion cell plasmodesmata connection(Xoconostle-Cazares, B., et al., (1999) Science 283:94-98). Some plantviruses have been shown to be able to establish systemic infections viamovement proteins (MP) that have the capacity to interact with theplasmodemata and foster the cell-cell transport of MP and viral nucleicacids. Thus plant viruses have evolved the capacity to utilize existingplant pathways to traffic macromolecules to surrounding cells. Plantsappear to have proteins similar to viral movement proteins that functionin the transport of nucleic acids from cell to cell. Several plant genesthat encode viral movement protein homologs have been identified in rice(elicitor-responsive gene 3, Os-FIERG1 and Os-FIERG2), one has beenidentified in corn (novel gene) and one has been identified in Cucurbitamaxima (CmPP16) (Xoconostle-Cazares, B., et al., (1999) Science283:94-98). Interestingly, movement of RNA throughout the plant ispostulated by some to explain the phenomena of cosuppression. Thus,understanding plant viral movement protein homologs and how they workwill provide mechanisms to control cosuppression and provide mechanismsto engineer plant virus resistance.

RNA-directed RNA polymerase (RdRP) is a plant-specific nucleicacid-synthesizing enzyme. Plants (tomato, chinese cabbage, cowpea,cauliflower, tobacco, and cucumber) are the only eukaryotes in whichcellular RdRP has demonstrated Schiebel W., et al., (1998) Plant Cell10:2087-2101) and furthermore, RdRP does not appear to be anRNA-dependent RNA polymerase, an enzyme that mediates viral RNAreplication. The origin and biological function of the enzyme however isunknown. Studies on the antiviral state in transgenic plants suggestthat RdRP could play a role in post-transcriptional gene silencing. ThusRdRP might play an important regulatory role in gene expression becauseit can transcribe RNA sequences (from RNA molecules) that could controlthe synthesis of nucleic acids and their translation into proteins.Understanding the function of RdRP in plants could provide a valuabletool to control gene expression via cosuppression and provide mechanismsto engineer plant virus resistance.

SUMMARY OF THE INVENTION

The present invention concerns isolated polynucleotides comprising anucleotide sequence encoding a polypeptide having RNA-directed RNApolymerase activity, wherein the amino acid sequence of the polypeptideand the amino acid sequence of SEQ ID NO: 2, 4, 6, 10, 12 or 22 have atleast 80% sequence identity. It is preferred that the identity be atleast 85%, it is preferable if the identity is at least 90%, it is morepreferred that the identity be at least 95%. The present invention alsorelates to isolated polynucleotides comprising the complement of thenucleotide sequence. More specifically, the present invention concernsisolated polynucleotides encoding the polypeptide sequence of SEQ ID NO:2, 4, 6, 10, 12 or 22 or nucleotide sequences comprising the nucleotidesequence of SEQ ID NO: 1, 3,5,9, 11 or21.

In a first embodiment, the present invention includes an isolatedpolynucleotide comprising: (a) a nucleotide sequence encoding apolypeptide having RNA-directed RNA polymerase activity, wherein thepolypeptide has an amino acid sequence of at least 80%, 85%, 90%, or 95%sequence identity, based on the Clustal V method of alignment, whencompared to one of SEQ ID NO: 2, 4, 6, 10, 12 or 22, or (b) a complementof the nucleotide sequence, wherein the complement and the nucleotidesequence consist of the same number of nucleotides and are 100%complementary. The polypeptide preferably comprises the amino acidsequence of SEQ ID NO: 2, 4, 6, 10, 12 or 22. The nucleotide sequencepreferably comprises the nucleotide sequence of SEQ ID NO: 2, 4, 6, 10,12 or 22.

In a second embodiment, the present invention concerns a recombinant DNAconstruct comprising any of the isolated polynucleotides of the presentinvention operably linked to at least one regulatory sequence, and acell, a plant, and a seed comprising the recombinant DNA construct.

In a third embodiment, the present invention includes a vectorcomprising any of the isolated polynucleotides of the present invention.

In a fourth embodiment, the present invention concerns a method fortransforming a cell comprising transforming a cell with any of theisolated polynucleotides of the present invention. The cell transformedby this method is also included. Advantageously, the cell is eukaryotic,e.g., a yeast or plant cell, or prokaryotic, e.g., a bacterium.

In a fifth embodiment, the present invention includes a method forproducing a transgenic plant comprising transforming a plant cell withany of the isolated polynucleotides of the present invention andregenerating a plant from the transformed plant cell. The invention isalso directed to the transgenic plant produced by this method, and seedobtained from this transgenic plant.

In a sixth embodiment, the present invention concerns an isolatedpolypeptide having RNA-directed RNA polymerase activity, wherein thepolypeptide has an amino acid sequence of at least 80%, 85%, 90%, or 95%identity, based on the Clustal V method of alignment, when compared toone of SEQ ID NO: 2, 4, 6, 10, 12 or 22. The polypeptide preferablycomprises one of SEQ ID NO: 2, 4, 6, 10, 12 or 22.

In a seventh embodiment, the present invention includes to a method forisolating a polypeptide having RNA-directed RNA polymerase activitycomprising isolating the polypeptide from a cell or culture medium ofthe cell, wherein the cell comprises a recombinant DNA constructcomprising a polynucleotide of the invention operably linked to at leastone regulatory sequence.

In an eighth embodiment, this invention concerns a method for selectinga transformed cell comprising: (a) transforming a host cell with therecombinant DNA construct or an expression cassette of the presentinvention; and (b) growing the transformed host cell, preferably a plantcell, under conditions that allow expression of the RNA-directed RNApolymerase polynucleotide in an amount sufficient to complement a nullmutant in order to provide a positive selection means.

In a ninth embodiment, this invention concerns a method of altering thelevel of expression of a RNA-directed RNA polymerase protein in a hostcell comprising: (a) transforming a host cell with a recombinant DNAconstruct of the present invention; and (b) growing the transformed hostcell under conditions that are suitable for expression of therecombinant DNA construct wherein expression of the recombinant DNAconstruct results in production of altered levels of the RNA-directedRNA polymerase protein in the transformed host cell.

A further embodiment of the instant invention is a method for evaluatingat least one compound for its ability to inhibit the activity of anRNA-directed RNA polymerase, the method comprising the steps of: (a)introducing into a host cell a recombinant DNA construct comprising anucleic acid fragment encoding an RNA-directed RNA polymerasepolypeptide, operably linked to at least one regulatory sequence; (b)growing the host cell under conditions that are suitable for expressionof the recombinant DNA construct wherein expression of the recombinantDNA construct results in production of RNA-directed RNA polymerasepolypeptide in the host cell; (c) optionally purifying the RNA-directedRNA polymerase polypeptide expressed by recombinant DNA construct in thehost cell; (d) treating the RNA-directed RNA polymerase polypeptide witha compound to be tested; (e) comparing the activity of the RNA-directedRNA polymerase polypeptide that has been treated with a test compound tothe activity of an untreated RNA-directed RNA polymerase polypeptide,and (f) selecting compounds with potential for inhibitory activity.

BRIEF DESCRIPTION OF THE SEQUENCE LISTINGS

The invention can be more fully understood from the following detaileddescription and the accompanying Sequence Listing which form a part ofthis application.

Table 1 lists the polypeptides that are described herein, thedesignation of the cDNA clones that comprise the nucleic acid fragmentsencoding polypeptides representing all or a substantial portion of thesepolypeptides, and the corresponding identifier (SEQ ID NO:) as used inthe attached Sequence Listing. Table 1 also identifies the cDNA clonesas individual ESTs (“EST”), the sequences of the entire cDNA insertscomprising the indicated cDNA clones (“FIS”), contigs assembled from twoor more ESTs (“Contig”), contigs assembled from an FIS and one or moreESTs (“Contig*”), or sequences encoding the entire protein derived froman FIS, a contig, or an FIS and PCR (“CGS”). Nucleotide sequences, SEQID NOs:7, 9 and 11 and amino acid sequences SEQ ID NOs:8, 10 and 12 weredetermined by further sequence analysis of cDNA clones encoding theamino acid sequences set forth in SEQ ID NOs:14, 16,18 and 20.Nucleotide SEQ ID NOs:13, 15, 17 and 19 and amino acid SEQ ID NOs: 14,16, 18 and 20 were among those disclosed in a U.S. ProvisionalApplication No. 60/128,094, filed Apr. 7, 1999. Nucleotide SEQ ID NOs:1, 3, 5, 7, 9 and 11 and amino acid SEQ ID NOs:2, 4, 6, 8, 10 and 12were among those disclosed in a U.S. patent application Ser. No.09/958,109, filed Oct. 2, 2001. Nucleotide SEQ ID NO:7 has sequencingerrors; the corrected nucleotide sequence is presented in SEQ ID NO:21,and the corresponding amino acid sequence is presented in SEQ ID NO:22.

The sequence descriptions and Sequence Listing attached hereto complywith the rules governing nucleotide and/or amino acid sequencedisclosures in patent applications as set forth in 37 C.F.R.§1.821-1.825.

TABLE 1 RNA-Directed RNA Polymerase Proteins SEQ ID NO: (Nucleo- (AminoProtein Clone Designation tide) Acid) RNA Directed cho1c.pk006.o1 (EST)1 2 RNA Polymerase RNA Directed Contig Composed of: 3 4 RNA Polymerasecpc1c.pk005.14 (EST) cpj1c.pk002.f24 (EST) p0005.cbmev75r (EST)p0031.ccmad44r (EST) p0049.curau90r (EST) RNA Directed Contig (CGS)Composed of: 5 6 RNA Polymerase p0016.ctsbo73r (FIS) PCR fragments RNADirected Contig (CGS) Composed of: 7 8 RNA Polymerase p0128.cpidb20r(FIS) PCR fragments RNA Directed rsl1n.pk014.o23 (FIS) 9 10 RNAPolymerase RNA Directed Contig (CGS) composed of: 11 12 RNA Polymerasesdp2c.pk007.l21 (FIS) sdp2c.pk029.f24 (FIS) sdp3c.pk022.g17 (FIS) PCRfragments RNA Directed Contig Composed of: 13 14 RNA Polymerasep0085.cscao73r (EST) p0086.cbsan57r (EST) p0099.ctbah82r (EST)p0107.cbcal33r (EST) p0128.cpiax70r (EST) p0128.cpidd23r (EST)p0128.cpidb20r (EST) RNA Directed rsl1n.pk014.o23 (EST) 15 16 RNAPolymerase RNA Directed sdp2c.pk007.l21 (EST) 17 18 RNA Polymerase RNADirected sdp3c.pk022.g17 (EST) 19 20 RNA Polymerase RNA Directed Contig(CGS) Composed of: 21 22 RNA Polymerase p0128.cpidb20r (FIS) PCRfragments

The Sequence Listing contains the one letter code for nucleotidesequence characters and the three letter codes for amino acids asdefined in conformity with the IUPAC-IUBMB standards described inNucleic Acids Res. 13:3021-3030 (1985) and in the Biochemical J. 219(No. 2):345-373 (1984) which are herein incorporated by reference. Thesymbols and format used for nucleotide and amino acid sequence datacomply with the rules set forth in 37 C.F.R. §1.822.

DETAILED DESCRIPTION OF THE INVENTION

In the context of this disclosure, a number of terms shall be utilized.The terms “polynucleotide”, “polynucleotide sequence”, “nucleic acidsequence”, and “nucleic acid fragment”/“isolated nucleic acid fragment”are used interchangeably herein. These terms encompass nucleotidesequences and the like. A polynucleotide may be a polymer of RNA or DNAthat is single- or double-stranded, that optionally contains synthetic,non-natural or altered nucleotide bases. A polynucleotide in the form ofa polymer of DNA may be comprised of one or more segments of cDNA,genomic DNA, synthetic DNA, or mixtures thereof. An isolatedpolynucleotide of the present invention may include at least one of 60contiguous nucleotides, preferably at least one of 40 contiguousnucleotides, most preferably one of at least 30 contiguous nucleotidesderived from SEQ ID NOs: 1, 3, 5, 9, 11 or 21 or the complement of suchsequences.

The term “isolated polynucleotide” refers to a polynucleotide that issubstantially free from other nucleic acid sequences, such as and notlimited to other chromosomal and extrachromosomal DNA and RNA. Isolatedpolynucleotides may be purified from a host cell in which they naturallyoccur. Conventional nucleic acid purification methods known to skilledartisans may be used to obtain isolated polynucleotides. The term alsoembraces recombinant polynucleotides and chemically synthesizedpolynucleotides.

The term “recombinant” means, for example, that a nucleic acid sequenceis made by an artificial combination of two otherwise separated segmentsof sequence, e.g., by chemical synthesis or by the manipulation ofisolated nucleic acids by genetic engineering techniques. A “recombinantDNA construct” comprises any of the isolated polynucleotides of thepresent invention operably linked to at least one regulatory sequence.

As used herein, “contig” refers to a nucleotide sequence that isassembled from two or more constituent nucleotide sequences that sharecommon or overlapping regions of sequence homology. For example, thenucleotide sequences of two or more nucleic acid fragments can becompared and aligned in order to identify common or overlappingsequences. Where common or overlapping sequences exist between two ormore nucleic acid fragments, the sequences (and thus their correspondingnucleic acid fragments) can be assembled into a single contiguousnucleotide sequence.

As used herein, “substantially similar” refers to nucleic acid fragmentswherein changes in one or more nucleotide bases results in substitutionof one or more amino acids, but does not affect the functionalproperties of the polypeptide encoded by the nucleotide sequence.“Substantially similar” also refers to nucleic acid fragments whereinchanges in one or more nucleotide bases does not affect the ability ofthe nucleic acid fragment to mediate alteration of gene expression bygene silencing through for example antisense or co-suppressiontechnology. “Substantially similar” also refers to modifications of thenucleic acid fragments of the instant invention such as deletion orinsertion of one or more nucleotides that do not substantially affectthe functional properties of the resulting transcript vis-à-vis theability to mediate gene silencing or alteration of the functionalproperties of the resulting protein molecule. It is therefore understoodthat the invention encompasses more than the specific exemplarynucleotide or amino acid sequences and includes functional equivalentsthereof. The terms “substantially similar” and “correspondingsubstantially” are used interchangeably herein.

Substantially similar nucleic acid fragments may be selected byscreening nucleic acid fragments representing subfragments ormodifications of the nucleic acid fragments of the instant invention,wherein one or more nucleotides are substituted, deleted and/orinserted, for their ability to affect the level of the polypeptideencoded by the unmodified nucleic acid fragment in a plant or plantcell. For example, a substantially similar nucleic acid fragmentrepresenting at least one of 30 contiguous nucleotides derived from theinstant nucleic acid fragment can be constructed and introduced into aplant or plant cell. The level of the polypeptide encoded by theunmodified nucleic acid fragment present in a plant or plant cellexposed to the substantially similar nucleic fragment can then becompared to the level of the polypeptide in a plant or plant cell thatis not exposed to the substantially similar nucleic acid fragment.

For example, it is well known in the art that antisense suppression andco-suppression of gene expression may be accomplished using nucleic acidfragments representing less than the entire coding region of a gene, andby using nucleic acid fragments that do not share 100% sequence identitywith the gene to be suppressed. Moreover, alterations in a nucleic acidfragment which result in the production of a chemically equivalent aminoacid at a given site, but do not effect the functional properties of theencoded polypeptide, are well known in the art. Thus, a codon for theamino acid alanine, a hydrophobic amino acid, may be substituted by acodon encoding another less hydrophobic residue, such as glycine, or amore hydrophobic residue, such as valine, leucine, or isoleucine.Similarly, changes which result in substitution of one negativelycharged residue for another, such as aspartic acid for glutamic acid, orone positively charged residue for another, such as lysine for arginine,can also be expected to produce a functionally equivalent product.Nucleotide changes which result in alteration of the N-terminal andC-terminal portions of the polypeptide molecule would also not beexpected to alter the activity of the polypeptide. Each of the proposedmodifications is well within the routine skill in the art, as isdetermination of retention of biological activity of the encodedproducts. Consequently, an isolated polynucleotide comprising anucleotide sequence of at least one of 60 (preferably at least one of40, most preferably at least one of 30) contiguous nucleotides derivedfrom a nucleotide sequence selected from the group consisting of SEQ IDNOs: 1, 3, 5, 9, 11 or 21 and the complement of such nucleotidesequences may be used in methods of selecting an isolated polynucleotidethat affects the expression of a RNA-directed RNA polymerase polypeptidein a host cell. A method of selecting an isolated polynucleotide thataffects the level of expression of a polypeptide in a virus or in a hostcell (eukaryotic, such as plant or yeast, prokaryotic such as bacterial)may comprise the steps of: constructing an isolated polynucleotide ofthe present invention or a chimeric gene of the present invention;introducing the isolated polynucleotide or the chimeric gene into a hostcell; measuring the level of a polypeptide or enzyme activity in thehost cell containing the isolated polynucleotide; and comparing thelevel of a polypeptide or enzyme activity in the host cell containingthe isolated polynucleotide with the level of a polypeptide or enzymeactivity in a host cell that does not contain the isolatedpolynucleotide.

Moreover, substantially similar nucleic acid fragments may also becharacterized by their ability to hybridize. Estimates of such homologyare provided by either DNA-DNA or DNA-RNA hybridization under conditionsof stringency as is well understood by those skilled in the art (Hamesand Higgins, Eds. (1985) Nucleic Acid Hybridisation, IRL Press, Oxford,U.K.). Stringency conditions can be adjusted to screen for moderatelysimilar fragments, such as homologous sequences from distantly relatedorganisms, to highly similar fragments, such as genes that duplicatefunctional enzymes from closely related organisms. Post-hybridizationwashes determine stringency conditions. One set of preferred conditionsuses a series of washes starting with 6×SSC, 0.5% SDS at roomtemperature for 15 min, then repeated with 2×SSC, 0.5% SDS at 45° C. for30 min, and then repeated twice with 0.2×SSC, 0.5% SDS at 50° C. for 30min. A more preferred set of stringent conditions uses highertemperatures in which the washes are identical to those above except forthe temperature of the final two 30 min washes in 0.2×SSC, 0.5% SDS wasincreased to 60° C. Another preferred set of highly stringent conditionsuses two final washes in 0.1×SSC, 0.1% SDS at 65° C.

Substantially similar nucleic acid fragments of the instant inventionmay also be characterized by the percent identity of the amino acidsequences that they encode to the amino acid sequences disclosed herein,as determined by algorithms commonly employed by those skilled in thisart. Suitable nucleic acid fragments (isolated polynucleotides of thepresent invention) encode polypeptides that are at least about 70%identical, preferably at least about 80% identical to the amino acidsequences reported herein. Preferred nucleic acid fragments encode aminoacid sequences that are about 85% identical to the amino acid sequencesreported herein. More preferred nucleic acid fragments encode amino acidsequences that are at least about 90% identical to the amino acidsequences reported herein. Most preferred are nucleic acid fragmentsthat encode amino acid sequences that are at least about 95% identicalto the amino acid sequences reported herein. Suitable nucleic acidfragments not only have the above identities but typically encode apolypeptide having at least 50 amino acids, preferably at least 100amino acids, more preferably at least 150 amino acids, still morepreferably at least 200 amino acids, and most preferably at least 250amino acids. Sequence alignments and percent identity calculations wereperformed using the Megalign program of the LASERGENE bioinformaticscomputing suite (DNASTAR Inc., Madison, Wis.). Multiple alignment of thesequences was performed using the Clustal V method of alignment (Higginsand Sharp (1989) CABIOS. 5:151-153) with the default parameters (GAPPENALTY=10, GAP LENGTH PENALTY=10). Default parameters for pairwisealignments using the Clustal V method were KTUPLE 1, GAP PENALTY=3,WINDOW=5 and DIAGONALS SAVED=5.

A “substantial portion” of an amino acid or nucleotide sequencecomprises an amino acid or a nucleotide sequence that is sufficient toafford putative identification of the protein or gene that the aminoacid or nucleotide sequence comprises. Amino acid and nucleotidesequences can be evaluated either manually by one skilled in the art, orby using computer-based sequence comparison and identification toolsthat employ algorithms such as BLAST (Basic Local Alignment Search Tool;Altschul et al. (1993) J. Mol. Biol. 215:403-410). In general, asequence of ten or more contiguous amino acids or thirty or morecontiguous nucleotides is necessary in order to putatively identify apolypeptide or nucleic acid sequence as homologous to a known protein orgene. Moreover, with respect to nucleotide sequences, gene-specificoligonucleotide probes comprising 30 or more contiguous nucleotides maybe used in sequence-dependent methods of gene identification (e.g.,Southern hybridization) and isolation (e.g., in situ hybridization ofbacterial colonies or bacteriophage plaques). In addition, shortoligonucleotides of 12 or more nucleotides may be used as amplificationprimers in PCR in order to obtain a particular nucleic acid fragmentcomprising the primers. Accordingly, a “substantial portion” of anucleotide sequence comprises a nucleotide sequence that will affordspecific identification and/or isolation of a nucleic acid fragmentcomprising the sequence. The instant specification teaches amino acidand nucleotide sequences encoding polypeptides that comprise one or moreparticular plant proteins. The skilled artisan, having the benefit ofthe sequences as reported herein, may now use all or a substantialportion of the disclosed sequences for purposes known to those skilledin this art. Accordingly, the instant invention comprises the completesequences as reported in the accompanying Sequence Listing, as well assubstantial portions of those sequences as defined above. “Codondegeneracy” refers to divergence in the genetic code permittingvariation of the nucleotide sequence without effecting the amino acidsequence of an encoded polypeptide. Accordingly, the instant inventionrelates to any nucleic acid fragment comprising a nucleotide sequencethat encodes all or a substantial portion of the amino acid sequencesset forth herein. The skilled artisan is well aware of the “codon-bias”exhibited by a specific host cell in usage of nucleotide codons tospecify a given amino acid. Therefore, when synthesizing a nucleic acidfragment for improved expression in a host cell, it is desirable todesign the nucleic acid fragment such that its frequency of codon usageapproaches the frequency of preferred codon usage of the host cell.“Synthetic nucleic acid fragments” can be assembled from oligonucleotidebuilding blocks that are chemically synthesized using procedures knownto those skilled in the art. These building blocks are ligated andannealed to form larger nucleic acid fragments which may then beenzymatically assembled to construct the entire desired nucleic acidfragment. “Chemically synthesized”, as related to a nucleic acidfragment, means that the component nucleotides were assembled in vitro.Manual chemical synthesis of nucleic acid fragments may be accomplishedusing well established procedures, or automated chemical synthesis canbe performed using one of a number of commercially available machines.Accordingly, the nucleic acid fragments can be tailored for optimal geneexpression based on optimization of the nucleotide sequence to reflectthe codon bias of the host cell. The skilled artisan appreciates thelikelihood of successful gene expression if codon usage is biasedtowards those codons favored by the host. Determination of preferredcodons can be based on a survey of genes derived from the host cellwhere sequence information is available.

“Gene” refers to a nucleic acid fragment that expresses a specificprotein, including regulatory sequences preceding (5′ non-codingsequences) and following (3′ non-coding sequences) the coding sequence.“Native gene” refers to a gene as found in nature with its ownregulatory sequences. “Chimeric gene” refers any gene that is not anative gene, comprising regulatory and coding sequences that are notfound together in nature. Accordingly, a chimeric gene may compriseregulatory sequences and coding sequences that are derived fromdifferent sources, or regulatory sequences and coding sequences derivedfrom the same source, but arranged in a manner different than that foundin nature. “Endogenous gene” refers to a native gene in its naturallocation in the genome of an organism. A “foreign gene” refers to a genenot normally found in the host organism, but that is introduced into thehost organism by gene transfer. Foreign genes can comprise native genesinserted into a non-native organism, or chimeric genes. A “transgene” isa gene that has been introduced into the genome by a transformationprocedure.

“Coding sequence” refers to a nucleotide sequence that codes for aspecific amino acid sequence. “Regulatory sequences” refer to nucleotidesequences located upstream (5′ non-coding sequences), within, ordownstream (3′ non-coding sequences) of a coding sequence, and whichinfluence the transcription, RNA processing or stability, or translationof the associated coding sequence. Regulatory sequences may includepromoters, translation leader sequences, introns, and polyadenylationrecognition sequences.

“Promoter” refers to a nucleotide sequence capable of controlling theexpression of a coding sequence or functional RNA. In general, a codingsequence is located 3′ to a promoter sequence. The promoter sequenceconsists of proximal and more distal upstream elements, the latterelements often referred to as enhancers. Accordingly, an “enhancer” is anucleotide sequence which can stimulate promoter activity and may be aninnate element of the promoter or a heterologous element inserted toenhance the level or tissue-specificity of a promoter. Promoters may bederived in their entirety from a native gene, or may be composed ofdifferent elements derived from different promoters found in nature, ormay even comprise synthetic nucleotide segments. It is understood bythose skilled in the art that different promoters may direct theexpression of a gene in different tissues or cell types, or at differentstages of development, or in response to different environmentalconditions. Promoters which cause a nucleic acid fragment to beexpressed in most cell types at most times are commonly referred to as“constitutive promoters”. New promoters of various types useful in plantcells are constantly being discovered; numerous examples may be found inthe compilation by Okamuro and Goldberg (1989) Biochemistry of Plants15:1-82. It is further recognized that since in most cases the exactboundaries of regulatory sequences have not been completely defined,nucleic acid fragments of different lengths may have identical promoteractivity. “Translation leader sequence” refers to a nucleotide sequencelocated between the promoter sequence of a gene and the coding sequence.The translation leader sequence is present in the fully processed mRNAupstream of the translation start sequence. The translation leadersequence may affect processing of the primary transcript to mRNA, mRNAstability or translation efficiency. Examples of translation leadersequences have been described (Turner and Foster (1995) Mol. Biotechnol.3:225-236).

“3′ non-coding sequences” refers to nucleotide sequences locateddownstream of a coding sequence and includes polyadenylation recognitionsequences and other sequences encoding regulatory signals capable ofaffecting mRNA processing or gene expression. The polyadenylation signalis usually characterized by affecting the addition of polyadenylic acidtracts to the 3′ end of the mRNA precursor. The use of different 3′non-coding sequences is exemplified by Ingelbrecht et al. (1989) PlantCell 1:671-680.

“RNA transcript” refers to the product resulting from RNApolymerase-catalyzed transcription of a DNA sequence. When the RNAtranscript is a perfect complementary copy of the DNA sequence, it isreferred to as the primary transcript or it may be a RNA sequencederived from posttranscriptional processing of the primary transcriptand is referred to as the mature RNA. “Messenger RNA (mRNA)” refers tothe RNA that is without introns and that can be translated intopolypeptides by the cell. “cDNA” refers to DNA that is complementary toand derived from an mRNA template. The cDNA can be single-stranded orconverted to double stranded form using, for example, the Klenowfragment of DNA polymerase I. “Sense RNA” refers to an RNA transcriptthat includes the mRNA and so can be translated into a polypeptide bythe cell. “Antisense RNA” refers to an RNA transcript that iscomplementary to all or part of a target primary transcript or mRNA andthat blocks the expression of a target gene (see U.S. Pat. No.5,107,065, incorporated herein by reference). The complementarity of anantisense RNA may be with any part of the specific nucleotide sequence,i.e., at the 5′ non-coding sequence, 3′ non-coding sequence, introns, orthe coding sequence. “Functional RNA” refers to sense RNA, antisenseRNA, ribozyme RNA, or other RNA that may not be translated but yet hasan effect on cellular processes.

The term “operably linked” refers to the association of two or morenucleic acid fragments so that the function of one is affected by theother. For example, a promoter is operably linked with a coding sequencewhen it is capable of affecting the expression of that coding sequence(i.e., that the coding sequence is under the transcriptional control ofthe promoter). Coding sequences can be operably linked to regulatorysequences in sense or antisense orientation.

The term “expression”, as used herein, refers to the transcription andstable accumulation of sense (mRNA) or antisense RNA derived from thenucleic acid fragment of the invention. “Expression” may also refer totranslation of mRNA into a polypeptide. “Antisense inhibition” refers tothe production of antisense RNA transcripts capable of suppressing theexpression of the target protein. “Overexpression” refers to theproduction of a gene product in transgenic organisms that exceeds levelsof production in normal or non-transformed organisms. “Co-suppression”refers to the production of sense RNA transcripts capable of suppressingthe expression of identical or substantially similar foreign orendogenous genes (U.S. Pat. No. 5,231,020, incorporated herein byreference).

A “protein” or “polypeptide” is a chain of amino acids arranged in aspecific order determined by the coding sequence in a polynucleotideencoding the polypeptide. Each protein or polypeptide has a uniquefunction.

“Altered levels” or “altered expression” refers to the production ofgene product(s) in transgenic organisms in amounts or proportions thatdiffer from that of normal or non-transformed organisms.

“Null mutant” refers to a host cell which either lacks the expression ofa certain polypeptide or expresses a polypeptide which is inactive ordoes not have any detectable expected enzymatic function.

“Mature protein” refers to a post-translationally processed polypeptide;i.e., one from which any pre- or propeptides present in the primarytranslation product have been removed. “Precursor protein” refers to theprimary product of translation of mRNA; i.e., with pre- and propeptidesstill present. Pre- and propeptides may be but are not limited tointracellular localization signals.

“Transformation” refers to the transfer of a nucleic acid fragment intothe genome of a host organism, resulting in genetically stableinheritance. Host organisms containing the transformed nucleic acidfragments are referred to as “transgenic” organisms. Examples of methodsof plant transformation include Agrobacterium-mediated transformation(De Blaere et al. (1987) Meth. Enzymol. 143:277) andparticle-accelerated or “gene gun” transformation technology (Klein etal. (1987) Nature (London) 327:70-73; U.S. Pat. No. 4,945,050,incorporated herein by reference). Thus, isolated polynucleotides of thepresent invention can be incorporated into recombinant constructs,typically DNA constructs, capable of introduction into and replicationin a host cell. Such a construct can be a vector that includes areplication system and sequences that are capable of transcription andtranslation of a polypeptide-encoding sequence in a given host cell. Anumber of vectors suitable for stable transfection of plant cells or forthe establishment of transgenic plants have been described in, e.g.,Pouwels et al., Cloning Vectors: A Laboratory Manual, 1985, supp. 1987;Weissbach and Weissbach, Methods for Plant Molecular Biology, AcademicPress, 1989; and Flevin et al., Plant Molecular Biology Manual, KluwerAcademic Publishers, 1990. Typically, plant expression vectors include,for example, one or more cloned plant genes under the transcriptionalcontrol of 5′ and 3′ regulatory sequences and a dominant selectablemarker. Such plant expression vectors also can contain a promoterregulatory region (e.g., a regulatory region controlling inducible orconstitutive, environmentally- or developmentally-regulated, or cell- ortissue-specific expression), a transcription initiation start site, aribosome binding site, an RNA processing signal, a transcriptiontermination site, and/or a polyadenylation signal.

Standard recombinant DNA and molecular cloning techniques used hereinare well known in the art and are described more fully in Sambrook etal. Molecular Cloning: A Laboratory Manual; Cold Spring HarborLaboratory Press: Cold Spring Harbor, 1989 (hereinafter “Maniatis”).

“PCR” or “polymerase chain reaction” is well known by those skilled inthe art as a technique used for the amplification of specific DNAsegments (U.S. Pat. Nos. 4,683,195 and 4,800,159).

The present invention concerns an isolated polynucleotide comprising anucleotide sequence selected from the group consisting of: (a) a firstnucleotide sequence encoding a polypeptide of at least 157 amino acidshaving at least 80% identity based on the Clustal V method of alignmentwhen compared to a polypeptide selected from the group consisting of SEQID NOs: 2, 4, 6, 10, 12 or 22, or (b) a second nucleotide sequencecomprising the complement of the first nucleotide sequence.

Preferably, the first nucleotide sequence comprises a nucleic acidsequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 9,11 or 21, that codes for the polypeptide selected from the groupconsisting of SEQ ID NOs2, 4, 6, 10, 12 or 22.

This invention also includes to the isolated complement of suchpolynucleotides, wherein the complement and the polynucleotide consistof the same number of nucleotides, and the nucleotide sequences of thecomplement and the polynucleotide have 100% complementarity.

Nucleic acid fragments encoding at least a portion of severalRNA-directed RNA polymerase proteins have been isolated and identifiedby comparison of random plant cDNA sequences to public databasescontaining nucleotide and protein sequences using the BLAST algorithmswell known to those skilled in the art. The nucleic acid fragments ofthe instant invention may be used to isolate cDNAs and genes encodinghomologous proteins from the same or other plant species. Isolation ofhomologous genes using sequence-dependent protocols is well known in theart. Examples of sequence-dependent protocols include, but are notlimited to, methods of nucleic acid hybridization, and methods of DNAand RNA amplification as exemplified by various uses of nucleic acidamplification technologies (e.g., polymerase chain reaction, ligasechain reaction).

For example, genes encoding other RNA-directed RNA polymerase proteins,either as cDNAs or genomic DNAs, could be isolated directly by using allor a portion of the instant nucleic acid fragments as DNA hybridizationprobes to screen libraries from any desired plant employing methodologywell known to those skilled in the art. Specific oligonucleotide probesbased upon the instant nucleic acid sequences can be designed andsynthesized by methods known in the art (Maniatis). Moreover, the entiresequence(s) can be used directly to synthesize DNA probes by methodsknown to the skilled artisan such as random primer DNA labeling, nicktranslation, end-labeling techniques, or RNA probes using available invitro transcription systems. In addition, specific primers can bedesigned and used to amplify a part or all of the instant sequences. Theresulting amplification products can be labeled directly duringamplification reactions or labeled after amplification reactions, andused as probes to isolate full length cDNA or genomic fragments underconditions of appropriate stringency.

In addition, two short segments of the instant nucleic acid fragmentsmay be used in polymerase chain reaction protocols to amplify longernucleic acid fragments encoding homologous genes from DNA or RNA. Thepolymerase chain reaction may also be performed on a library of clonednucleic acid fragments wherein the sequence of one primer is derivedfrom the instant nucleic acid fragments, and the sequence of the otherprimer takes advantage of the presence of the polyadenylic acid tractsto the 3′ end of the mRNA precursor encoding plant genes. Alternatively,the second primer sequence may be based upon sequences derived from thecloning vector. For example, the skilled artisan can follow the RACEprotocol (Frohman et al. (1988) Proc. Natl. Acad. Sci. USA 85:8998-9002)to generate cDNAs by using PCR to amplify copies of the region between asingle point in the transcript and the 3′ or 5′ end. Primers oriented inthe 3′ and 5′ directions can be designed from the instant sequences.Using commercially available 3′ RACE or 5′ RACE systems (BRL), specific3′ or 5′ cDNA fragments can be isolated (Ohara et al. (1989) Proc. Natl.Acad. Sci. USA 86:5673-5677; Loh et al. (1989) Science 243:217-220).Products generated by the 3′ and 5′ RACE procedures can be combined togenerate full-length cDNAs (Frohman and Martin (1989) Techniques 1:165).Consequently, a polynucleotide comprising a nucleotide sequence of atleast one of 60 (preferably one of at least 40, most preferably one ofat least 30) contiguous nucleotides derived from a nucleotide sequenceselected from the group consisting of SEQ ID NOs: 1, 3, 5, 9, 11 or 21and the complement of such nucleotide sequences may be used in suchmethods to obtain a nucleic acid fragment encoding a substantial portionof an amino acid sequence of a polypeptide.

The present invention relates to a method of obtaining a nucleic acidfragment encoding a substantial portion of a RNA-directed RNA polymerasepolypeptide, preferably a substantial portion of a plant RNA-directedRNA polymerase polypeptide, comprising the steps of: synthesizing anoligonucleotide primer comprising a nucleotide sequence of at least oneof 60 (preferably at least one of 40, most preferably at least one of30) contiguous nucleotides derived from a nucleotide sequence selectedfrom the group consisting of SEQ ID NOs: 1, 3, 5, 9, 11 or 21, and thecomplement of such nucleotide sequences; and amplifying a nucleic acidfragment (preferably a cDNA inserted in a cloning vector) using theoligonucleotide primer. The amplified nucleic acid fragment preferablywill encode a portion of a RNA-directed RNA polymerase polypeptide.

Availability of the instant nucleotide and deduced amino acid sequencesfacilitates immunological screening of cDNA expression libraries.Synthetic peptides representing portions of the instant amino acidsequences may be synthesized. These peptides can be used to immunizeanimals to produce polyclonal or monoclonal antibodies with specificityfor peptides or proteins comprising the amino acid sequences. Theseantibodies can be then be used to screen cDNA expression libraries toisolate full-length cDNA clones of interest (Lerner (1984) Adv. Immunol.36:1-34; Maniatis).

In another embodiment, this invention concerns viruses and host cellscomprising either the chimeric genes of the invention as describedherein or an isolated polynucleotide of the invention as describedherein. Examples of host cells which can be used to practice theinvention include, but are not limited to, yeast, bacteria, and plants.

As was noted above, the nucleic acid fragments of the instant inventionmay be used to create transgenic plants in which the disclosedpolypeptides are present at higher or lower levels than normal or incell types or developmental stages in which they are not normally found.This would have the effect of altering the level of RNA-directed RNApolymerase activity in those cells.

Overexpression of the proteins of the instant invention may beaccomplished by first constructing a chimeric gene in which the codingregion is operably linked to a promoter capable of directing expressionof a gene in the desired tissues at the desired stage of development.The chimeric gene may comprise promoter sequences and translation leadersequences derived from the same genes. 3′ Non-coding sequences encodingtranscription termination signals may also be provided. The instantchimeric gene may also comprise one or more introns in order tofacilitate gene expression.

Plasmid vectors comprising the instant isolated polynucleotide (orchimeric gene) may be constructed. The choice of plasmid vector isdependent upon the method that will be used to transform host plants.The skilled artisan is well aware of the genetic elements that must bepresent on the plasmid vector in order to successfully transform, selectand propagate host cells containing the chimeric gene. The skilledartisan will also recognize that different independent transformationevents will result in different levels and patterns of expression (Joneset al. (1985) EMBO J. 4:2411-2418; De Almeida et al. (1989) Mol. Gen.Genetics 218:78-86), and thus that multiple events must be screened inorder to obtain lines displaying the desired expression level andpattern. Such screening may be accomplished by Southern analysis of DNA,Northern analysis of mRNA expression, Western analysis of proteinexpression, or phenotypic analysis.

It may also be desirable to reduce or eliminate expression of genesencoding the instant polypeptides in plants for some applications. Inorder to accomplish this, a chimeric gene designed for co-suppression ofthe instant polypeptide can be constructed by linking a gene or genefragment encoding that polypeptide to plant promoter sequences.Alternatively, a chimeric gene designed to express antisense RNA for allor part of the instant nucleic acid fragment can be constructed bylinking the gene or gene fragment in reverse orientation to plantpromoter sequences. Either the co-suppression or antisense chimericgenes could be introduced into plants via transformation whereinexpression of the corresponding endogenous genes are reduced oreliminated.

Molecular genetic solutions to the generation of plants with alteredgene expression have a decided advantage over more traditional plantbreeding approaches. Changes in plant phenotypes can be produced byspecifically inhibiting expression of one or more genes by antisenseinhibition or cosuppression (U.S. Pat. Nos. 5,190,931, 5,107,065 and5,283,323). An antisense or cosuppression construct would act as adominant negative regulator of gene activity. While conventionalmutations can yield negative regulation of gene activity these effectsare most likely recessive. The dominant negative regulation availablewith a transgenic approach may be advantageous from a breedingperspective. In addition, the ability to restrict the expression of aspecific phenotype to the reproductive tissues of the plant by the useof tissue specific promoters may confer agronomic advantages relative toconventional mutations which may have an effect in all tissues in whicha mutant gene is ordinarily expressed.

The person skilled in the art will know that special considerations areassociated with the use of antisense or cosuppression technologies inorder to reduce expression of particular genes. For example, the properlevel of expression of sense or antisense genes may require the use ofdifferent chimeric genes utilizing different regulatory elements knownto the skilled artisan. Once transgenic plants are obtained by one ofthe methods described above, it will be necessary to screen individualtransgenics for those that most effectively display the desiredphenotype. Accordingly, the skilled artisan will develop methods forscreening large numbers of transformants. The nature of these screenswill generally be chosen on practical grounds. For example, one canscreen by looking for changes in gene expression by using antibodiesspecific for the protein encoded by the gene being suppressed, or onecould establish assays that specifically measure enzyme activity. Apreferred method will be one which allows large numbers of samples to beprocessed rapidly, since it will be expected that a large number oftransformants will be negative for the desired phenotype.

In another embodiment, the present invention concerns a polypeptide ofat least 157 amino acids that has at least 80% identity based on theClustal V method of alignment when compared to a polypeptide selectedfrom the group consisting of SEQ ID NOs: 2, 4, 6, 10, 12 or 22.

The instant polypeptides (or portions thereof) may be produced inheterologous host cells, particularly in the cells of microbial hosts,and can be used to prepare antibodies to the proteins by methods wellknown to those skilled in the art. The antibodies are useful fordetecting the polypeptides of the instant invention in situ in cells orin vitro in cell extracts. Preferred heterologous host cells forproduction of the instant polypeptides are microbial hosts. Microbialexpression systems and expression vectors containing regulatorysequences that direct high level expression of foreign proteins are wellknown to those skilled in the art. Any of these could be used toconstruct a chimeric gene for production of the instant polypeptides.This chimeric gene could then be introduced into appropriatemicroorganisms via transformation to provide high level expression ofthe encoded RNA-directed RNA polymerase protein. An example of a vectorfor high level expression of the instant polypeptides in a bacterialhost is provided (Example 6).

All or a substantial portion of the polynucleotides of the instantinvention may also be used as probes for genetically and physicallymapping the genes that they are a part of, and used as markers fortraits linked to those genes. Such information may be useful in plantbreeding in order to develop lines with desired phenotypes. For example,the instant nucleic acid fragments may be used as restriction fragmentlength polymorphism (RFLP) markers. Southern blots (Maniatis) ofrestriction-digested plant genomic DNA may be probed with the nucleicacid fragments of the instant invention. The resulting banding patternsmay then be subjected to genetic analyses using computer programs suchas MapMaker (Lander et al. (1987) Genomics 1:174-181) in order toconstruct a genetic map. In addition, the nucleic acid fragments of theinstant invention may be used to probe Southern blots containingrestriction endonuclease-treated genomic DNAs of a set of individualsrepresenting parent and progeny of a defined genetic cross. Segregationof the DNA polymorphisms is noted and used to calculate the position ofthe instant nucleic acid sequence in the genetic map previously obtainedusing this population (Botstein et al. (1980) Am. J. Hum. Genet.32:314-331).

The production and use of plant gene-derived probes for use in geneticmapping is described in Bernatzky and Tanksley (1986) Plant Mol. Biol.Reporter 4:37-41. Numerous publications describe genetic mapping ofspecific cDNA clones using the methodology outlined above or variationsthereof. For example, F2 intercross populations, backcross populations,randomly mated populations, near isogenic lines, and other sets ofindividuals may be used for mapping. Such methodologies are well knownto those skilled in the art.

Nucleic acid probes derived from the instant nucleic acid sequences mayalso be used for physical mapping (i.e., placement of sequences onphysical maps; see Hoheisel et al. In: Nonmammalian Genomic Analysis: APractical Guide, Academic press 1996, pp. 319-346, and references citedtherein).

In another embodiment, nucleic acid probes derived from the instantnucleic acid sequences may be used in direct fluorescence in situhybridization (FISH) mapping (Trask (1991) Trends Genet. 7:149-154).Although current methods of FISH mapping favor use of large clones(several to several hundred KB; see Laan et al. (1995) Genome Res.5:13-20), improvements in sensitivity may allow performance of FISHmapping using shorter probes.

A variety of nucleic acid amplification-based methods of genetic andphysical mapping may be carried out using the instant nucleic acidsequences. Examples include allele-specific amplification (Kazazian(1989) J. Lab. Clin. Med. 11:95-96), polymorphism of PCR-amplifiedfragments (CAPS; Sheffield et al. (1993) Genomics 16:325-332),allele-specific ligation (Landegren et al. (1988) Science241:1077-1080), nucleotide extension reactions (Sokolov (1990) NucleicAcid Res. 18:3671), Radiation Hybrid Mapping (Walter et al. (1997) Nat.Genet. 7:22-28) and Happy Mapping (Dear and Cook (1989) Nucleic AcidRes. 17:6795-6807). For these methods, the sequence of a nucleic acidfragment is used to design and produce primer pairs for use in theamplification reaction or in primer extension reactions. The design ofsuch primers is well known to those skilled in the art. In methodsemploying PCR-based genetic mapping, it may be necessary to identify DNAsequence differences between the parents of the mapping cross in theregion corresponding to the instant nucleic acid sequence. This,however, is generally not necessary for mapping methods.

Loss of function mutant phenotypes may be identified for the instantcDNA clones either by targeted gene disruption protocols or byidentifying specific mutants for these genes contained in a maizepopulation carrying mutations in all possible genes (Ballinger andBenzer (1989) Proc. Natl. Acad. Sci USA 86:9402-9406; Koes et al. (1995)Proc. Natl. Acad. Sci USA 92:8149-8153; Bensen et al. (1995) Plant Cell7:75-84). The latter approach may be accomplished in two ways. First,short segments of the instant nucleic acid fragments may be used inpolymerase chain reaction protocols in conjunction with a mutation tagsequence primer on DNAs prepared from a population of plants in whichMutator transposons or some other mutation-causing DNA element has beenintroduced (see Bensen, supra). The amplification of a specific DNAfragment with these primers indicates the insertion of the mutation tagelement in or near the plant gene encoding the instant polypeptides.Alternatively, the instant nucleic acid fragment may be used as ahybridization probe against PCR amplification products generated fromthe mutation population using the mutation tag sequence primer inconjunction with an arbitrary genomic site primer, such as that for arestriction enzyme site-anchored synthetic adaptor. With either method,a plant containing a mutation in the endogenous gene encoding theinstant polypeptides can be identified and obtained. This mutant plantcan then be used to determine or confirm the natural function of theinstant polypeptides disclosed herein.

EXAMPLES

The present invention is further defined in the following Examples, inwhich parts and percentages are by weight and degrees are Celsius,unless otherwise stated. It should be understood that these Examples,while indicating preferred embodiments of the invention, are given byway of illustration only. From the above discussion and these Examples,one skilled in the art can ascertain the essential characteristics ofthis invention, and without departing from the spirit and scope thereof,can make various changes and modifications of the invention to adapt itto various usages and conditions. Thus, various modifications of theinvention in addition to those shown and described herein will beapparent to those skilled in the art from the foregoing description.Such modifications are also intended to fall within the scope of theappended claims.

The disclosure of each reference set forth herein is incorporated hereinby reference in its entirety.

Example 1 Composition of cDNA Libraries; Isolation and Sequencing ofcDNA Clones

cDNA libraries representing mRNAs from various corn, rice and soybeantissues were prepared. The characteristics of the libraries aredescribed below.

TABLE 2 cDNA Libraries from Corn, Rice and Soybean Library Tissue Clonecho1c Corn Embryo 20 Days After Pollination cho1c.pk006.o1 cpc1c Cornpooled BMS treated with chemicals cpc1c.pk005.l4 related to cGMP** cpj1cCorn Pooled BMS Treated With cpj1c.pk002.f24 Chemicals Related toMembrane Ionic Force*** p0005 Corn Immature Ear p0005.cbmev75r p0016Corn Tassel Shoots, Pooled, 0.1-1.4 cm p0016.ctsbo73r p0031 Corn ShootCulture p0031.ccmad44r p0049 Corn Whole Kernels 5 Days Afterp0049.curau90r Pollination p0128 Corn Primary and Secondary Immaturep0128.cpidb20r Ear rsl1n Rice 15-Day-Old Seedling* rsl1n.pk014.o23 sdp2cSoybean Developing Pods (6-7 mm) sdp2c.pk007.l21 sdp2c.pk029.f24 sdp3cSoybean Developing Pods (8-9 mm) sdp3c.pk022.g17 *This library wasnormalized essentially as described in U.S. Pat. No. 5,482,845,incorporated herein by reference. **Chemicals used included suramin,MAS7, dipyryridamole, zaprinast, 8-bromo cGMPtrequinsin HCl, compound48/80 ***Chemicals used included valinomycin, bafilomycin Al,oligomycin, ionomycin

cDNA libraries may be prepared by any one of many methods available. Forexample, the cDNAs may be introduced into plasmid vectors by firstpreparing the cDNA libraries in Uni-ZAP™ XR vectors according to themanufacturer's protocol (Stratagene Cloning Systems, La Jolla, Calif.).The Uni-ZAP™ XR libraries are converted into plasmid libraries accordingto the protocol provided by Stratagene. Upon conversion, cDNA insertswill be contained in the plasmid vector pBluescript. In addition, thecDNAs may be introduced directly into precut Bluescript II SK(+) vectors(Stratagene) using T4 DNA ligase (New England Biolabs), followed bytransfection into DH10B cells according to the manufacturer's protocol(GIBCO BRL Products). Once the cDNA inserts are in plasmid vectors,plasmid DNAs are prepared from randomly picked bacterial coloniescontaining recombinant pBluescript plasmids, or the insert cDNAsequences are amplified via polymerase chain reaction using primersspecific for vector sequences flanking the inserted cDNA sequences.Amplified insert DNAs or plasmid DNAs are sequenced in dye-primersequencing reactions to generate partial cDNA sequences (expressedsequence tags or “ESTs”; see Adams et al., (1991) Science252:1651-1656). The resulting ESTs are analyzed using a Perkin ElmerModel 377 fluorescent sequencer.

Full-insert sequence (FIS) data is generated utilizing a modifiedtransposition protocol. Clones identified for FIS are recovered fromarchived glycerol stocks as single colonies, and plasmid DNAs areisolated via alkaline lysis. Isolated DNA templates are reacted withvector primed M13 forward and reverse oligonucleotides in a PCR-basedsequencing reaction and loaded onto automated sequencers. Confirmationof clone identification is performed by sequence alignment to theoriginal EST sequence from which the FIS request is made.

Confirmed templates are transposed via the Primer Island transpositionkit (PE Applied Biosystems, Foster City, Calif.) which is based upon theSaccharomyces cerevisiae Ty1 transposable element (Devine and Boeke(1994) Nucleic Acids Res. 22:3765-3772). The in vitro transpositionsystem places unique binding sites randomly throughout a population oflarge DNA molecules. The transposed DNA is then used to transform DH10Belectro-competent cells (Gibco BRL/Life Technologies, Rockville, Md.)via electroporation. The transposable element contains an additionalselectable marker (named DHFR; Fling and Richards (1983) Nucleic AcidsRes. 11:5147-5158), allowing for dual selection on agar plates of onlythose subclones containing the integrated transposon. Multiple subclonesare randomly selected from each transposition reaction, plasmid DNAs areprepared via alkaline lysis, and templates are sequenced (ABI Prismdye-terminator ReadyReaction mix) outward from the transposition eventsite, utilizing unique primers specific to the binding sites within thetransposon.

Sequence data is collected (ABI Prism Collections) and assembled usingPhred and Phrap (Ewing et al. (1998) Genome Res. 8:175-185; Ewing andGreen (1998) Genome Res. 8:186-194). Phred is a public domain softwareprogram which re-reads the ABI sequence data, re-calls the bases,assigns quality values, and writes the base calls and quality valuesinto editable output files. The Phrap sequence assembly program usesthese quality values to increase the accuracy of the assembled sequencecontigs. Assemblies are viewed by the Consed sequence editor (Gordon etal. (1998) Genome Res. 8:195-202).

In some of the clones the cDNA fragment corresponds to a portion of the3′-terminus of the gene and does not cover the entire open readingframe. In order to obtain the upstream information one of two differentprotocols are used. The first of these methods results in the productionof a fragment of DNA containing a portion of the desired gene sequencewhile the second method results in the production of a fragmentcontaining the entire open reading frame. Both of these methods use tworounds of PCR amplification to obtain fragments from one or morelibraries. The libraries some times are chosen based on previousknowledge that the specific gene should be found in a certain tissue andsome times are randomly-chosen. Reactions to obtain the same gene may beperformed on several libraries in parallel or on a pool of libraries.Library pools are normally prepared using from 3 to 5 differentlibraries and normalized to a uniform dilution. In the first round ofamplification both methods use a vector-specific (forward) primercorresponding to a portion of the vector located at the 5′-terminus ofthe clone coupled with a gene-specific (reverse) primer. The firstmethod uses a sequence that is complementary to a portion of the alreadyknown gene sequence while the second method uses a gene-specific primercomplementary to a portion of the 3′-untranslated region (also referredto as UTR). In the second round of amplification a nested set of primersis used for both methods. The resulting DNA fragment is ligated into apBluescript vector using a commercial kit and following themanufacturer's protocol. This kit is selected from many available fromseveral vendors including Invitrogen (Carlsbad, Calif.), Promega Biotech(Madison, Wis.), and Gibco-BRL (Gaithersburg, Md.). The plasmid DNA isisolated by alkaline lysis method and submitted for sequencing andassembly using Phred/Phrap, as above.

Example 2 Identification of cDNA Clones

cDNA clones encoding RNA-directed RNA polymerase proteins wereidentified by conducting BLAST (Basic Local Alignment Search Tool;Altschul et al. (1993) J. Mol. Biol. 215:403-410) searches forsimilarity to sequences contained in the BLAST “nr” database (comprisingall non-redundant GenBank CDS translations, sequences derived from the3-dimensional structure Brookhaven Protein Data Bank, the last majorrelease of the SWISS-PROT protein sequence database, EMBL, and DDBJdatabases). The cDNA sequences obtained in Example 1 were analyzed forsimilarity to all publicly available DNA sequences contained in the “nr”database using the BLASTN algorithm provided by the National Center forBiotechnology Information (NCBI). The DNA sequences were translated inall reading frames and compared for similarity to all publicly availableprotein sequences contained in the “nr” database using the BLASTXalgorithm (Gish and States (1993) Nat. Genet. 3:266-272) provided by theNCBI. For convenience, the P-value (probability) of observing a match ofa cDNA sequence to a sequence contained in the searched databases merelyby chance as calculated by BLAST are reported herein as “pLog” values,which represent the negative of the logarithm of the reported P-value.Accordingly, the greater the pLog value, the greater the likelihood thatthe cDNA sequence and the BLAST “hit” represent homologous proteins.

Example 3 Characterization of cDNA Clones Encoding RNA-Directed RNAPolymerase

The BLASTX search using the EST sequences from clones listed in Table 3revealed similarity of the polypeptides encoded by the cDNAs toRNA-directed RNA polymerase from Arabidopsis thaliana (NCBI IdentifierNo. gi 3600048), Arabidopsis thaliana (NCBI Identifier No. gi 3687225),Arabidopsis thaliana (NCBI Identifier No. gi 6553930) and Nicotianatabacum (NCBI Identifier No. gi 4138282). Shown in Table 3 are the BLASTresults for individual ESTs (“EST”), the sequences of the entire cDNAinserts comprising the indicated cDNA clones (“FIS”), contigs assembledfrom two or more ESTs (“Contig”), contigs assembled from an FIS and oneor more ESTs (“Contig*”), or sequences encoding the entire proteinderived from an FIS, a contig, or an FIS and PCR (“CGS”):

TABLE 3 BLAST Results for Sequences Encoding Polypeptides Homologous toArabidopsis thaliana and Nicotiana tabacum RNA-Directed RNA PolymeraseClone Status BLAST pLog Score cho1c.pk006.o1 EST 34.70 (gi 3687225)Contig Composed of: Contig 169.00 (gi 3600048) cpc1c.pk005.14 (EST)cpj1c.pk002.f24 (EST) p0005.cbmev75r (EST) p0031.ccmad44r (EST)p0049.curau90r (EST) p0016.ctsbo73r CGS >254.00 (gi 4138282)p0128.cpidb20r CGS >254.00 (gi 6553930) rsl1n.pk014.o23 FIS >254.00 (gi6553930) Contig composed of: CGS >254.00 (gi 4138282) sdp2c.pk007.l21(FIS) sdp2c.pk029.f24 (FIS) sdp3c.pk022.g17 (FIS)

Nucleotide SEQ ID NO:7 and the corresponding amino acid sequence SEQ IDNO:8, 10 presented in U.S. patent application Ser. No. 09/958,109, filedOct. 2, 2001, were found to have sequencing errors. A correctednucleotide sequence is presented in SEQ ID NO:21, and the correspondingcorrected amino acid sequence is presented in SEQ ID NO:22.

The data in Table 4 represents a calculation of the percent identity ofthe amino acid sequences set forth in SEQ ID NOs:2, 4, 6, 8, 10, 12 and22 and the Arabidopsis thaliana and Nicotiana tabacum sequences.

TABLE 4 Percent Identity of Amino Acid Sequences Deduced From theNucleotide Sequences of cDNA Clones Encoding Polypeptides Homologous toArabidopsis thaliana and Nicotiana tabacum RNA-Directed RNA PolymeraseSEQ ID NO. Percent Identity to 2 46% (gi 3687225) 4 58% (gi 3600048) 653% (gi 4138282) 8 53% (gi 6553930) 10 61% (gi 6553930) 12 59% (gi4138282) 22 55% (gi 6553930)

Sequence alignments and percent identity calculations were performedusing the Megalign program of the LASERGENE bioinformatics computingsuite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the sequenceswas performed using the Clustal V method of alignment (Higgins and Sharp(1989) CABIOS. 5:151-153) with the default parameters (GAP PENALTY=10,GAP LENGTH PENALTY=10). Default parameters for pairwise alignments usingthe Clustal V method were KTUPLE 1, GAP PENALTY=3, WINDOW=5 andDIAGONALS SAVED=5. Sequence alignments, BLAST scores and probabilitiesindicate that the nucleic acid fragments comprising the instant cDNAclones encode a substantial portion of a RNA-directed RNA polymerase.

Example 4 Expression of Chimeric Genes in Monocot Cells

A chimeric gene comprising a cDNA encoding the instant polypeptides insense orientation with respect to the maize 27 kD zein promoter that islocated 5′ to the cDNA fragment, and the 10 kD zein 3′ end that islocated 3′ to the cDNA fragment, can be constructed. The cDNA fragmentof this gene may be generated by polymerase chain reaction (PCR) of thecDNA clone using appropriate oligonucleotide primers. Cloning sites(NcoI or SmaI) can be incorporated into the oligonucleotides to provideproper orientation of the DNA fragment when inserted into the digestedvector pML103 as described below. Amplification is then performed in astandard PCR. The amplified DNA is then digested with restrictionenzymes NcoI and SmaI and fractionated on an agarose gel. Theappropriate band can be isolated from the gel and combined with a 4.9 kbNcoI-SmaI fragment of the plasmid pML103. Plasmid pML103 has beendeposited under the terms of the Budapest Treaty at ATCC (American TypeCulture Collection, 10801 University Blvd., Manassas, Va. 20110-2209),and bears accession number ATCC 97366. The DNA segment from pML103contains a 1.05 kb SalI-NcoI promoter fragment of the maize 27 kD zeingene and a 0.96 kb SmaI-SalI fragment from the 3′ end of the maize 10 kDzein gene in the vector pGem9Zf(+) (Promega). Vector and insert DNA canbe ligated at 15° C. overnight, essentially as described (Maniatis). Theligated DNA may then be used to transform E. coli XL1-Blue (EpicurianColi XL-1 Blue™; Stratagene). Bacterial transformants can be screened byrestriction enzyme digestion of plasmid DNA and limited nucleotidesequence analysis using the dideoxy chain termination method (Sequenase™DNA Sequencing Kit; U.S. Biochemical). The resulting plasmid constructwould comprise a chimeric gene encoding, in the 5′ to 3′ direction, themaize 27 kD zein promoter, a cDNA fragment encoding the instantpolypeptides, and the 10 kD zein 3′ region.

The chimeric gene described above can then be introduced into corn cellsby the following procedure. Immature corn embryos can be dissected fromdeveloping caryopses derived from crosses of the inbred corn lines H99and LH132. The embryos are isolated 10 to 11 days after pollination whenthey are 1.0 to 1.5 mm long. The embryos are then placed with theaxis-side facing down and in contact with agarose-solidified N6 medium(Chu et al. (1975) Sci. Sin. Peking 18:659-668). The embryos are kept inthe dark at 27° C. Friable embryogenic callus consisting ofundifferentiated masses of cells with somatic proembryoids and embryoidsborne on suspensor structures proliferates from the scutellum of theseimmature embryos. The embryogenic callus isolated from the primaryexplant can be cultured on N6 medium and sub-cultured on this mediumevery 2 to 3 weeks.

The plasmid, p35S/Ac (obtained from Dr. Peter Eckes, Hoechst Ag,Frankfurt, Germany) may be used in transformation experiments in orderto provide for a selectable marker. This plasmid contains the Pat gene(see European Patent Publication 0 242 236) which encodesphosphinothricin acetyl transferase (PAT). The enzyme PAT confersresistance to herbicidal glutamine synthetase inhibitors such asphosphinothricin. The pat gene in p35S/Ac is under the control of the35S promoter from Cauliflower Mosaic Virus (Odell et al. (1985) Nature313:810-812) and the 3′ region of the nopaline synthase gene from theT-DNA of the Ti plasmid of Agrobacterium tumefaciens.

The particle bombardment method (Klein et al. (1987) Nature 327:70-73)may be used to transfer genes to the callus culture cells. According tothis method, gold particles (1 μm in diameter) are coated with DNA usingthe following technique. Ten μg of plasmid DNAs are added to 50 μL of asuspension of gold particles (60 mg per mL). Calcium chloride (50 μL ofa 2.5 M solution) and spermidine free base (20 μL of a 1.0 M solution)are added to the particles. The suspension is vortexed during theaddition of these solutions. After 10 minutes, the tubes are brieflycentrifuged (5 sec at 15,000 rpm) and the supernatant removed. Theparticles are resuspended in 200 μL of absolute ethanol, centrifugedagain and the supernatant removed. The ethanol rinse is performed againand the particles resuspended in a final volume of 30 μL of ethanol. Analiquot (5 μL) of the DNA-coated gold particles can be placed in thecenter of a Kapton™ flying disc (Bio-Rad Labs). The particles are thenaccelerated into the corn tissue with a Biolistic™ PDS-1000/He (Bio-RadInstruments, Hercules Calif.), using a helium pressure of 1000 psi, agap distance of 0.5 cm and a flying distance of 1.0 cm.

For bombardment, the embryogenic tissue is placed on filter paper overagarose-solidified N6 medium. The tissue is arranged as a thin lawn andcovered a circular area of about 5 cm in diameter. The petri dishcontaining the tissue can be placed in the chamber of the PDS-1000/Heapproximately 8 cm from the stopping screen. The air in the chamber isthen evacuated to a vacuum of 28 inches of Hg. The macrocarrier isaccelerated with a helium shock wave using a rupture membrane thatbursts when the He pressure in the shock tube reaches 1000 psi.

Seven days after bombardment the tissue can be transferred to N6 mediumthat contains gluphosinate (2 mg per liter) and lacks casein or proline.The tissue continues to grow slowly on this medium. After an additional2 weeks the tissue can be transferred to fresh N6 medium containinggluphosinate. After 6 weeks, areas of about 1 cm in diameter of activelygrowing callus can be identified on some of the plates containing theglufosinate-supplemented medium. These calli may continue to grow whensub-cultured on the selective medium.

Plants can be regenerated from the transgenic callus by firsttransferring clusters of tissue to N6 medium supplemented with 0.2 mgper liter of 2,4-D. After two weeks the tissue can be transferred toregeneration medium (Fromm et al. (1990) Bio/Technology 8:833-839).

Example 5 Expression of Chimeric Genes in Dicot Cells

A seed-specific construct composed of the promoter and transcriptionterminator from the gene encoding the β subunit of the seed storageprotein phaseolin from the bean Phaseolus vulgaris (Doyle et al. (1986)J. Biol. Chem. 261:9228-9238) can be used for expression of the instantpolypeptides in transformed soybean. The phaseolin construct includesabout 500 nucleotides upstream (5′) from the translation initiationcodon and about 1650 nucleotides downstream (3′) from the translationstop codon of phaseolin. Between the 5′ and 3′ regions are the uniquerestriction endonuclease sites Nco I (which includes the ATG translationinitiation codon), Sma I, Kpn I and Xba I. The entire construct isflanked by Hind III sites.

The cDNA fragment of this gene may be generated by polymerase chainreaction (PCR) of the cDNA clone using appropriate oligonucleotideprimers. Cloning sites can be incorporated into the oligonucleotides toprovide proper orientation of the DNA fragment when inserted into theexpression vector. Amplification is then performed as described above,and the isolated fragment is inserted into a pUC 18 vector carrying theseed construct.

Soybean embryos may then be transformed with the expression vectorcomprising sequences encoding the instant polypeptides. To inducesomatic embryos, cotyledons, 3-5 mm in length dissected from surfacesterilized, immature seeds of the soybean cultivar A2872, can becultured in the light or dark at 26° C. on an appropriate agar mediumfor 6-10 weeks. Somatic embryos which produce secondary embryos are thenexcised and placed into a suitable liquid medium. After repeatedselection for clusters of somatic embryos which multiplied as early,globular staged embryos, the suspensions are maintained as describedbelow.

Soybean embryogenic suspension cultures can be maintained in 35 mLliquid media on a rotary shaker, 150 rpm, at 26° C. with florescentlights on a 16:8 hour day/night schedule. Cultures are subcultured everytwo weeks by inoculating approximately 35 mg of tissue into 35 mL ofliquid medium.

Soybean embryogenic suspension cultures may then be transformed by themethod of particle gun bombardment (Klein et al. (1987) Nature (London)327:70-73, U.S. Pat. No. 4,945,050). A DuPont Biolistic™ PDS1000/HEinstrument (helium retrofit) can be used for these transformations.

A selectable marker gene which can be used to facilitate soybeantransformation is a chimeric gene composed of the 35S promoter fromCauliflower Mosaic Virus (Odell et al. (1985) Nature 313:810-812), thehygromycin phosphotransferase gene from plasmid pJR225 (from E. coli;Gritz et al.(1983) Gene 25:179-188) and the 3′ region of the nopalinesynthase gene from the T-DNA of the Ti plasmid of Agrobacteriumtumefaciens. The seed construct comprising the phaseolin 5′ region, thefragment encoding the instant polypeptides and the phaseolin 3′ regioncan be isolated as a restriction fragment. This fragment can then beinserted into a unique restriction site of the vector carrying themarker gene.

To 50 μL of a 60 mg/mL 1 μm gold particle suspension is added (inorder): 5 μL DNA (1 μg/μL), 20 μL spermidine (0.1 M), and 50 μL CaCl₂(2.5 M). The particle preparation is then agitated for three minutes,spun in a microfuge for 10 seconds and the supernatant removed. TheDNA-coated particles are then washed once in 400 μL 70% ethanol andresuspended in 40 μL of anhydrous ethanol. The DNA/particle suspensioncan be sonicated three times for one second each. Five μL of theDNA-coated gold particles are then loaded on each macro carrier disk.

Approximately 300-400 mg of a two-week-old suspension culture is placedin an empty 60×15 mm petri dish and the residual liquid removed from thetissue with a pipette. For each transformation experiment, approximately5-10 plates of tissue are normally bombarded. Membrane rupture pressureis set at 1100 psi and the chamber is evacuated to a vacuum of 28 inchesmercury. The tissue is placed approximately 3.5 inches away from theretaining screen and bombarded three times. Following bombardment, thetissue can be divided in half and placed back into liquid and culturedas described above.

Five to seven days post bombardment, the liquid media may be exchangedwith fresh media, and eleven to twelve days post bombardment with freshmedia containing 50 mg/mL hygromycin. This selective media can berefreshed weekly. Seven to eight weeks post bombardment, green,transformed tissue may be observed growing from untransformed, necroticembryogenic clusters. Isolated green tissue is removed and inoculatedinto individual flasks to generate new, clonally propagated, transformedembryogenic suspension cultures. Each new line may be treated as anindependent transformation event. These suspensions can then besubcultured and maintained as clusters of immature embryos orregenerated into whole plants by maturation and germination ofindividual somatic embryos.

Example 6 Expression of Chimeric Genes in Microbial Cells

The cDNAs encoding the instant polypeptides can be inserted into the T7E. coli expression vector pBT430. This vector is a derivative of pET-3a(Rosenberg et al. (1987) Gene 56:125-135) which employs thebacteriophage T7 RNA polymerase/T7 promoter system. Plasmid pBT430 wasconstructed by first destroying the EcoR I and Hind III sites in pET-3aat their original positions. An oligonucleotide adaptor containing EcoRI and Hind III sites was inserted at the BamH I site of pET-3a. Thiscreated pET-3aM with additional unique cloning sites for insertion ofgenes into the expression vector. Then, the Nde I site at the positionof translation initiation was converted to an Nco I site usingoligonucleotide-directed mutagenesis. The DNA sequence of pET-3aM inthis region, 5′-CATATGG, was converted to 5′-CCCATGG in pBT430.

Plasmid DNA containing a cDNA may be appropriately digested to release anucleic acid fragment encoding the protein. This fragment may then bepurified on a 1% NuSieve GTG™ low melting agarose gel (FMC). Buffer andagarose contain 10 μg/mL ethidium bromide for visualization of the DNAfragment. The fragment can then be purified from the agarose gel bydigestion with GELase™ (Epicentre Technologies) according to themanufacturer's instructions, ethanol precipitated, dried and resuspendedin 20 μL of water. Appropriate oligonucleotide adapters may be ligatedto the fragment using T4 DNA ligase (New England Biolabs, Beverly,Mass.). The fragment containing the ligated adapters can be purifiedfrom the excess adapters using low melting agarose as described above.The vector pBT430 is digested, dephosphorylated with alkalinephosphatase (NEB) and deproteinized with phenol/chloroform as describedabove. The prepared vector pBT430 and fragment can then be ligated at16° C. for 15 hours followed by transformation into DH5 electrocompetentcells (GIBCO BRL). Transformants can be selected on agar platescontaining LB media and 100 μg/mL ampicillin. Transformants containingthe gene encoding the instant polypeptides are then screened for thecorrect orientation with respect to the T7 promoter by restrictionenzyme analysis.

For high level expression, a plasmid clone with the cDNA insert in thecorrect orientation relative to the T7 promoter can be transformed intoE. coli strain BL21(DE3) (Studier et al. (1986) J. Mol. Biol.189:113-130). Cultures are grown in LB medium containing ampicillin (100mg/L) at 25° C. At an optical density at 600 nm of approximately 1, IPTG(isopropylthio-β-galactoside, the inducer) can be added to a finalconcentration of 0.4 mM and incubation can be continued for 3 h at 25°.Cells are then harvested by centrifugation and re-suspended in 50 μL of50 mM Tris-HCl at pH 8.0 containing 0. 1 mM DTT and 0.2 mM phenylmethylsulfonyl fluoride. A small amount of 1 mm glass beads can be addedand the mixture sonicated 3 times for about 5 seconds each time with amicroprobe sonicator. The mixture is centrifuged and the proteinconcentration of the supernatant determined. One μg of protein from thesoluble fraction of the culture can be separated by SDS-polyacrylamidegel electrophoresis. Gels can be observed for protein bands migrating atthe expected molecular weight.

1. An isolated polynucleotide comprising: (a) a nucleotide sequenceencoding a polypeptide having RNA-directed RNA polymerase activity,wherein the polypeptide has an amino acid sequence of at least 80%sequence identity, based on the Clustal V method of alignment withpairwise alignment default parameters of KTUPLE=1, GAP PENALTY=3,WINDOW=5 and DIAGONALS SAVED=5, when compared to one of SEQ ID NO:2, 4,6, 10, 12 or 22, or (b) a complement of the nucleotide sequence, whereinthe complement and the nucleotide sequence consist of the same number ofnucleotides and are 100% complementary.
 2. The polynucleotide of claim1, wherein the amino acid sequence of the polypeptide has at least 85%sequence identity, based on the Clustal V method of alignment with thedefault pairwise alignment parameters, when compared to one of SEQ IDNO: 2, 4, 6, 10, 12 or
 22. 3. The polynucleotide of claim 1, wherein theamino acid sequence of the polypeptide has at least 90% sequenceidentity, based on the Clustal V method of alignment with the defaultpairwise alignment parameters, when compared to one of SEQ ID NO: 2, 4,6, 10, 12or22.
 4. The polynucleotide of claim 1, wherein the amino acidsequence of the polypeptide has at least 95% sequence identity, based onthe Clustal V method of alignment with the default pairwise alignmentparameters, when compared to one of SEQ ID NO: 2, 4, 6, 10, 12 or
 22. 5.The polynucleotide of claim 1, wherein the amino acid sequence of thepolypeptide comprises one of SEQ ID NO: 2, 4, 6, 10, 12 or
 22. 6. Thepolynucleotide of claim 1 wherein the nucleotide sequence comprises oneof SEQ ID NO:1, 3, 5, 9, 11 or21.
 7. A vector comprising thepolynucleotide of claim
 1. 8. A recombinant DNA construct comprising thepolynucleotide of claim 1 operably linked to at least one regulatorysequence.
 9. A method for transforming a cell, comprising transforming acell with the polynucleotide of claim
 1. 10. A cell comprising therecombinant DNA construct of claim
 8. 11. A method for producing atransgenic plant comprising transforming a plant cell with thepolynucleotide of claim 1 and regenerating a transgenic plant from thetransformed plant cell.
 12. A plant comprising the recombinant DNAconstruct of claim
 8. 13. A seed comprising the recombinant DNAconstruct of claim
 8. 14. An isolated polypeptide having RNA-dependentRNA polymerase activity, wherein the polypeptide has an amino acidsequence of at least 80% sequence identity, based on the Clustal Vmethod of alignment with pairwise alignment default parameters ofKTUPLE=1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5, when comparedto one of SEQ ID NO: 2, 4, 6, 10, 12 or
 22. 15. The polypeptide of claim14, wherein the amino acid sequence of the polypeptide has at least 85%sequence identity, based on the Clustal V method of alignment with thedefault pairwise alignment parameters, when compared to one of SEQ IDNO: 2, 4, 6, 10, 12 or22.
 16. The polypeptide of claim 14, wherein theamino acid sequence of the polypeptide has at least 90% sequenceidentity, based on the Clustal V method of alignment with the defaultpairwise alignment parameters, when compared to one of SEQ ID NO: 2, 4,6, 10, 12 or
 22. 17. The polypeptide of claim 14, wherein the amino acidsequence of the polypeptide has at least 95% sequence identity, based onthe Clustal V method of alignment with the default pairwise alignmentparameters, when compared to one of SEQ ID NO: 2, 4, 6, 10, 12 or 22.18. The polypeptide of claim 14, wherein the amino acid sequence of thepolypeptide comprises one of SEQ ID NO: 2, 4, 6, 10, 12 or
 22. 19. Amethod for isolating a polypeptide having RNA-dependent RNA polymeraseactivity comprising isolating the polypeptide from a cell or culturemedium of the cell, wherein the cell comprises a recombinant DNAconstruct comprising the polynucleotide of claim 1 operably linked to atleast one regulatory sequence.
 20. A method of altering the level ofexpression of an RNA-dependent RNA polymerase in a host cell comprising:(a) transforming a host cell with the recombinant DNA construct of claim8; and (b) growing the transformed host cell under conditions that aresuitable for expression of the recombinant DNA construct whereinexpression of the recombinant DNA construct results in production ofaltered levels of the RNA-dependent RNA polymerase in the transformedhost cell.